From 072de573ca196a792987225a6a1c76b45b7f3e67 Mon Sep 17 00:00:00 2001 From: "naumenko.sa" Date: Fri, 1 Feb 2019 16:03:22 -0500 Subject: [PATCH] added zygosity columns to the clinical report --- cre.topmed.R | 2 +- cre.vcf2db.R | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/cre.topmed.R b/cre.topmed.R index 0109779..e2578fa 100644 --- a/cre.topmed.R +++ b/cre.topmed.R @@ -20,7 +20,7 @@ get_af_by_rsid <- function(rs_id){ # from Johar 2016 # rs_id <- "rs202193903" # rs_id = "rs903331232" - rs_id = "rs1129038" + # rs_id = "rs1129038" #- not found #ls("package:MafDb.TOPMed.freeze5.hg19") mafdb <- MafDb.TOPMed.freeze5.hg19 diff --git a/cre.vcf2db.R b/cre.vcf2db.R index 509e804..bf6a784 100644 --- a/cre.vcf2db.R +++ b/cre.vcf2db.R @@ -671,7 +671,8 @@ clinical_report <- function(project,samples){ filtered_report <- subset(full_report, Quality > 1000 & Gnomad_af_popmax < 0.005 & Frequency_in_C4R < 6 & max_alt >=20, - select = c("Position", "GNOMAD_Link", "Ref", "Alt", "Gene", paste0("Burden.",samples), + select = c("Position", "GNOMAD_Link", "Ref", "Alt", "Gene", paste0("Zygosity.", samples), + paste0("Burden.",samples), "Variation", "Info", "Refseq_change", "Omim_gene_description", "Omim_inheritance", "Orphanet", "Clinvar", "Frequency_in_C4R", "Gnomad_af_popmax", "Gnomad_af", "Gnomad_ac", "Gnomad_hom",